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J.J. Nelson smiled. His thoughts on his soon-to-be 36-year-old quarterback racing toward the end zone for what turned out to be the game-winning touchdown?

“A sigh of relief,” Nelson said.

It’s hard to think of it any other way. This wasn’t like the 47-7 beatdown the Cardinals put on the 49ers back in September. San Francisco has a better quarterback behind center (I can’t believe I typed that, but it is true) than it did then. Still, the Cards only allowed 13 points. What was the cold water on the face Sunday was the Cards’ inability to consistently score and definitely the inability to generate a steady run game. That’s the first game all season Carson Palmer didn’t throw a touchdown pass. It’s so odd to think the Cards won the turnover battle for the first time a month-plus yet had to work so hard to finish off the Niners.

Here’s all you need to know: Bruce Arians gave the players a Victory Monday off — and immediately, Patrick Peterson jumped in and told the defensive players they have to be in by 11 Monday. “We’ve got to fix this,” he said.

— I’ve been wracking my brain since the sequence happened early in the second half, but I cannot remember a weirder sequence than the one during which the Cards scored their first touchdown – nor can I remember a sequence in both sides were frustrated.

It started with a first-and-goal at the SF 3. The Cardinals ended up running nine plays inside the 5. Four were from the 1. And the Cardinals couldn’t push it in. No worries – the 49ers were flagged for four penalties, including three pass interference calls, all of which were automatic first downs. The Cards even tried trickeration, putting Drew Stanton in at QB and splitting Palmer out wide as a receiver, only to have Stanton hand the ball to Chris Johnson for a one-yard loss.

— The plays spotlighted the short-yardage issues the Cards had all game trying to run. Ironic that the score eventually came via the ground, with David Johnson punching one over. But the line of scrimmage was not won by the Cardinals’ offensive line most of the game.

— The Cards ended up with bigger problems running backs-wise than just missed third-and-1 tries. Chris Johnson exited with a left knee injury, and on the same drive, Andre Ellington left with a right foot injury. Their status is TBD. There is a reason the Cardinals built their running back depth, and rookie David Johnson isn’t a bad guy to turn to if the other two are sidelined.

But it’s a concern. Johnson tweeted out a handful of praying hands emojis after the game, although he said he doesn’t think it’s serious. What he is praying about is left to the imagination for now. They will get fully evaluated back in Arizona. Johnson has had issues with his knee all week.

— Tyrann Mathieu was all over the field Sunday with 13 tackles and he picked off Gabbert. He wasn’t satisfied – he was upset he allowed the touchdown pass the 49ers had – but he continues to have an all-pro season.

— The thin cornerback corps could get thinner. Bruce Arians said the Cards are hoping Jerraud Powers’ injury is a calf and not an Achilles issue, but either way, it puts Justin Bethel up again. Thank goodness for the Cards that Patrick Peterson looked fine on his injured ankle.

— It turned out not to matter, but that missed extra point by Chandler Catanzaro really, really could’ve mattered. Cat Man sees again how you can go from hero to near-goat in an awful hurry as a kicker.

— Larry Fitzgerald had 14 targets and 10 catches. He never could get loose – with 66 yards, he is still eight yards shy of 1,000 for the season – but he became the short-yardage answer on third downs when the Cards realized they couldn’t run it.

— On eight run plays in which the Cardinals needed three yards or less, the Cards lost yards on five of them. They were stopped for no gain on two. The other was David Johnson’s one-yard TD at the end of that nine-plays-inside-the-5.

— The 49ers are ticked off about the officials. The Cardinals weren’t thrilled either, but certainly not to the level of the game’s loser. It was not a great day for the officials in terms of making things clear, but their calls impacted the game. No doubt about that. I didn’t get a chance to study the Dial hit on Palmer on replay, but it’s not surprising a flag would be thrown. That’s the NFL we live in these days.

— Wide receiver Smokey Brown looked better than he has in weeks, running full speed down the field, his hamstring apparently not a problem. “I’m almost there,” he said. He had five catches for 99 yards.

— The Seahawks came from behind to win. The Vikings won. It was an important day for the Cards not to give up ground. Now a trip to St. Louis, where physical is going to be the word of the day. More NFC West fun.

Bruce Arians is usually blunt, and he was again when assessing Patrick Peterson’s game in New York.

“I thought it was probably his poorest game since I’ve been here,” Arians said.

It wasn’t a good day for the Cardinals’ Pro Bowl cornerback. He was beaten on a (pretty and one-handed) seven-yard touchdown fade by big wide receiver Reuben Randle. The Giants got him on some other short stuff, and his physical play was not a good match for what the officials were calling. In total, there were five illegal contacts, five defensive holds and two pass interference calls against defenders trying to cover receivers for both teams. On the Giants’ second touchdown drive, Peterson was called for a defensive hold (teammate Jerraud Powers was called for one on the same play, too), setting off Peterson. In his anger he appeared to bump an official, although he was not flagged. And then a few plays later, he intentionally grabbed Victor Cruz in the end zone to prevent a TD pass, and the 25-yard penalty set up a one-yard TD toss.

Peterson was still fuming when he came to the bench, calmed down by, among others, injured teammate Darnell Dockett.

“He got frustrated and let the referees get to him,” Arians said.

The officials were given an edict from the league to crack down on such penalties. It’s not a surprise. Peterson gathered himself and when talking after the game, said exactly what needed to be said, which was that he needed to play within the rules as they are now being called.

“As a secondary, and as a defensive back, you have to adapt,” Peterson said. “There are no excuses. The way this league is an offensive league, they are trying to make the best way possible to get more points on the board because that’s what draws fans. I just have to be smart, I – we – just have to get our hands off the receivers, and just play smart football.”

That’s one area in which Arians will agree with. Arians said after the game the calls were correct, and he followed it up Monday by saying the officials called “a heck of a game.”

“The players played a bad one,” Arians said. “There was a lot of holding on both sides. We were as guilty as they were. The referees did a heck of a job, I thought, continuing to throw the flags because guys continued to grab. You better learn how to play with the rules.”

The NFL and the NFL Referees Association announced Wednesday night the two sides had finally come to an agreement and the regular officials are coming back. It won’t be ratified before Friday and Saturday, but commissioner Roger Goodell lifted the lockout so the game tomorrow night between the Browns and Ravens will be covered by the regular guys.

If nothing else, it takes away a huge distraction from the first few weeks of the season. It was inevitable after the mess Monday night in Seattle The Cardinals had been fortunate in their first three games since there really had been no major issues that affected the outcome (although the extra timeout the refs gave the Seahawks in the opener would have cost the Cards had the Seahawks won late, and imagine if Seattle was 3-0 with two wins it shouldn’t have.)

As it is, the blown call in the Seahawks-Packers game could hurt the Cardinals. The Seahawks are 2-1 and not 1-2 in the NFC West.

“Well it was upsetting, because it does affect us,” Cardinals quarterback Kevin Kolb said. “In my eyes, it was clearly an interception. Just like anybody else around, it’s something that doesn’t sit well with us, because it directly affects us. That’s unfortunate at this level.”

The Cardinals have been careful not to say much of anything on the subject (although Darnell Dockett did drop an expletive on Twitter Monday night — not that it mattered, because the NFL decided not to fine any players critical and Dockett wasn’t the only one to use such language.) Coach Ken Whisenhunt made sure the message was that the Cards couldn’t let it bother them, no matter who the officials were. “We just want the right calls to be made,” Kolb said.

The official press release listed these particulars for the new eight-year agreement:

The agreement includes the following key terms:

— The current defined benefit pension plan will remain in place for current officials through the 2016 season (or until the official earns 20 years of service). The defined benefit plan will then be frozen.

— Retirement benefits will be provided for new hires, and for all officials beginning in 2017, through a defined contribution arrangement, which will have two elements: an annual league contribution made on behalf of each game official that will begin with an average of more than $18,000 per official and increase to more than $23,000 per official in 2019, and a partial match on any additional contribution that an official makes to his 401(k) account.

— Apart from their benefit package, the game officials’ compensation will increase from an average of $149,000 a year in 2011 to $173,000 in 2013, rising to $205,000 by 2019.

— Beginning with the 2013 season, the NFL will have the option of hiring a number of officials on a full-time basis to work year-round, including on the field.

— The NFL will have the option to retain additional officials for training and development purposes, and may assign those additional officials to work NFL games. The number of additional officials will be determined by the NFL.

Those are details I’m sure most don’t care about. Most just care that the officials are back. And we’ll see how long it is before someone complains about one of the calls they make.

It rained all morning at the Cardinals’ Tempe facility Friday, all the way through practice. Yes, the Cardinals open up at home Sunday, but since a team from Seattle is the opponent, maybe the precipitation was fitting. I know that personally, it felt odd to have a steady downpour in early September. It seemed to dovetail a little bit with the uncertainty around the Cards going into the season.

Even coach Ken Whisenhunt noted “there is a lot more unknown with our team,” between how the new offensive line will hold up to John Skelton as cemented starter for the first time (remember last year, when Kevin Kolb was healthy, he was put back in the lineup). But Whiz did say “I think everyone is always optimistic going into the first game,” and I think that’s true. There is going to be a sense of us-against-the-world right now in the locker room. A lot of teams go down that road (even good teams that aren’t criticized much) but the Cards can definitely find bulletin-board material if they so choose.

— Beanie Wells ended up on the injury report today with a hamstring issue. He told Kent Somers he’d play, but he is listed as questionable. Interestingly, Wells has just missed three games in the last 30 the Cardinals have played – and each one has been against Seattle. He sat out the meaningless finale last year in UoP, but the game he missed in Seattle – because of a hamstring – ended up being crucial when the Cards lost by three and could have used their star back.

“It was frustrating for me in that particular game having to sit back and watch, not be able to help the team,” Wells said.

Veteran Chester Taylor was Wells’ replacement and couldn’t do anything. (LaRod Stephens-Howling, who had 93 yards rushing in the second Seattle game, was injured too.) Alfonso Smith did a decent job in relief, but the Cards certainly could have used Ryan Williams. If Beanie is limited or out Sunday, Williams will be there this time.

— Talking to Wells before the hamstring problem, I asked him how his recovery from his knee was. “I am getting there,” Beanie said. “I’m not going to say I am there yet, but it is definitely coming.”

— Williams, talking about his own recovery from his patella tendon issue: “I feel like I am a couple weeks away. With this injury, you are still going to feel some lingering pinching, things of that sort, I say since the Oakland game, maybe a week before, I have been really feeling like myself. I have made some moves in practice I have just been waiting to make. I feel like I used to, making cuts, and getting my football awareness, my football sense up under me.”

— Sam Rosen is doing the play by play for Fox for this game. Why does that matter? Rosen was doing the work in each of the four games Patrick Peterson returned a punt for a touchdown – and he was in the booth the last game of the year when Seattle visited, the game in which Peterson should have had a fifth TD if Seahawks punter Jon Ryan hadn’t somehow tripped him up with a fingernail or two.

— Lot of questions about this, but don’t forget: the NFL moved a handful of kickoff times this season on late games, and this is one of them. Kickoff is at 1:25 p.m., not 1:15 p.m. Make sure you check the homepage if there are ever any kickoff time questions.

— Whisenhunt said he had addressed his team before the Hall of Fame game about awareness of the replacement officials. There has not been and won’t be a follow-up. “It’s not something you talk about,” Whisenhunt said. “You don’t want to get too wrapped up in that.”

— We’ll see how rookie right tackle Bobby Massie and new left tackle D’Anthony Batiste hold up Sunday. Batiste, remember, has just four NFL starts, all at guard, all in 2007. Nothing changes in the scheme, offensive coordinator Mike Miller said, only some of the ways the Cards will protect it. The defensive front and the looks the Cards will see more or less dictates if the Cards will give one of their tackles help. “As (offensive line coach) Russ (Grimm) always says, on each play, someone is going to have a tough block,” Miller said.

— Defensive end Calais Campbell has six sacks in six career starts against the Seahawks. Why does he do so well against them? Don’t ask him. “I couldn’t tell you. I don’t know,” Campbell said, chuckling as he struggled to find a reason. “I try my hardest every time I’m out there. I don’t know how to answer that question – but I’m looking forward to seeing if I can do it again

— Another guy who has always killed the Seahawks has been Larry Fitzgerald, including last year’s finale when he exploded for 149 yards on nine catches and nearly single-handedly willed the Cards’ offense to a win. Fitz needs seven receptions to reach 700 in his career, and whether he gets it this week or next, he’ll be the youngest player ever to reach that mark. For his career – 16 games total – Fitz has 102 catches for 1,371 yards against Seattle, his top marks against any one franchise.

— Speaking of Wilson, defensive coordinator Ray Horton said he has the same mobility as last year’s Seattle starter, Tarvaris Jackson, but “he gets the ball out faster.” That said, Horton said he believes the Cards’ cornerbacks have more depth than last year. One thing to watch: Who the third cornerback is in the game. William Gay might start as No. 2, but based on the last couple of preseason games, the Cards may use Gay as a nickel and get rookie Jamell Fleming on the outside.

— The Cards need to be stout on the ground, which could be harder with the scrambling ability of Wilson. In the finale last year, Marshawn Lynch had 86 yards on 19 carries, and Leon Washington added 78 on seven carries. Now they have rookie Robert Turbin in the mix. Putting Wilson into uncomfortable, long passing situations starts with slowing the run game. Lynch is questionable with a back issue, but most Seattle writers are guessing he will play Sunday.